ProtoGuide: Prototype-Driven Guidance for Class-Conditional Graph Generation

Abstract:Discrete diffusion models are a prominent family for graph generation, but standard class-conditional mechanisms embed the class signal in the denoiser during training, tying the conditioning mechanism to the trained model. Classifier guidance avoids this coupling in continuous domains by steering a frozen model with a classifier's gradient, but discrete graph diffusion samples discrete edge states, so gradients cannot propagate through the sampled graph. We introduce ProtoGuide, a post-hoc, backbone-agnostic framework that recovers an analogous mechanism. At each reverse step the denoiser's per-edge output is relaxed into a differentiable soft adjacency, embedded by a frozen Siamese graph neural network, and scored against a target-class prototype and its nearest competitor; the resulting per-edge gradient, damped by a cosine schedule, is injected back into the denoiser output. All components stay frozen, so guidance is retargeted by supplying a different prototype. On five classes of real-world networks and two architecturally different backbones, EDGE and DiGress, ProtoGuide raises macro classification accuracy from 50.7% to 73.5% and from 73.6% to 83.8%, and outperforms DiGress's built-in conditional training under our configuration. Gains are largest where the unguided models are weakest, and are not uniform across classes. Per-graph coverage remains high in most settings, while distributional effects are class-dependent. A Best-of-N selection baseline matches this accuracy given enough oversampling, but at a substantial cost in graph diversity. An independently initialized classifier, a directionality test, and a few-shot analysis support target-directed steering and robustness to very small support sets.

Preprint. Submitted to IEEE Transactions on Pattern Analysis and Machine Intelligence. 35 pages, 2 figures, 33 tables

Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Physics and Society (physics.soc-ph)

arXiv:2609.15239 [cs.LG]

(or arXiv:2609.15239v1 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2609.15239 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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